Job ID = 5791780 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:40:56 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-22T01:42:52 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-22T01:42:52 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 6,793,044 reads read : 13,586,088 reads written : 13,586,088 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:52 6793044 reads; of these: 6793044 (100.00%) were paired; of these: 603908 (8.89%) aligned concordantly 0 times 5447102 (80.19%) aligned concordantly exactly 1 time 742034 (10.92%) aligned concordantly >1 times ---- 603908 pairs aligned concordantly 0 times; of these: 279859 (46.34%) aligned discordantly 1 time ---- 324049 pairs aligned 0 times concordantly or discordantly; of these: 648098 mates make up the pairs; of these: 509045 (78.54%) aligned 0 times 61720 (9.52%) aligned exactly 1 time 77333 (11.93%) aligned >1 times 96.25% overall alignment rate Time searching: 00:02:52 Overall time: 00:02:52 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 235601 / 6466650 = 0.0364 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 10:50:10: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:50:10: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:50:14: 1000000 INFO @ Wed, 22 Apr 2020 10:50:18: 2000000 INFO @ Wed, 22 Apr 2020 10:50:23: 3000000 INFO @ Wed, 22 Apr 2020 10:50:27: 4000000 INFO @ Wed, 22 Apr 2020 10:50:31: 5000000 INFO @ Wed, 22 Apr 2020 10:50:36: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:50:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 10:50:40: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:50:40: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:50:40: 7000000 INFO @ Wed, 22 Apr 2020 10:50:44: 1000000 INFO @ Wed, 22 Apr 2020 10:50:45: 8000000 INFO @ Wed, 22 Apr 2020 10:50:49: 2000000 INFO @ Wed, 22 Apr 2020 10:50:49: 9000000 INFO @ Wed, 22 Apr 2020 10:50:53: 3000000 INFO @ Wed, 22 Apr 2020 10:50:54: 10000000 INFO @ Wed, 22 Apr 2020 10:50:58: 4000000 INFO @ Wed, 22 Apr 2020 10:50:58: 11000000 INFO @ Wed, 22 Apr 2020 10:51:03: 5000000 INFO @ Wed, 22 Apr 2020 10:51:03: 12000000 INFO @ Wed, 22 Apr 2020 10:51:06: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 10:51:06: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 10:51:06: #1 total tags in treatment: 5958790 INFO @ Wed, 22 Apr 2020 10:51:06: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:51:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:51:06: #1 tags after filtering in treatment: 4521225 INFO @ Wed, 22 Apr 2020 10:51:06: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 10:51:06: #1 finished! INFO @ Wed, 22 Apr 2020 10:51:06: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:51:06: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 10:51:06: Too few paired peaks (28) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 10:51:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:51:07: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:51:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 10:51:10: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:51:10: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:51:12: 7000000 INFO @ Wed, 22 Apr 2020 10:51:14: 1000000 INFO @ Wed, 22 Apr 2020 10:51:16: 8000000 INFO @ Wed, 22 Apr 2020 10:51:19: 2000000 INFO @ Wed, 22 Apr 2020 10:51:21: 9000000 INFO @ Wed, 22 Apr 2020 10:51:24: 3000000 INFO @ Wed, 22 Apr 2020 10:51:25: 10000000 INFO @ Wed, 22 Apr 2020 10:51:28: 4000000 INFO @ Wed, 22 Apr 2020 10:51:30: 11000000 INFO @ Wed, 22 Apr 2020 10:51:33: 5000000 INFO @ Wed, 22 Apr 2020 10:51:35: 12000000 INFO @ Wed, 22 Apr 2020 10:51:37: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 10:51:37: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 10:51:37: #1 total tags in treatment: 5958790 INFO @ Wed, 22 Apr 2020 10:51:37: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:51:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:51:37: #1 tags after filtering in treatment: 4521225 INFO @ Wed, 22 Apr 2020 10:51:37: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 10:51:37: #1 finished! INFO @ Wed, 22 Apr 2020 10:51:37: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:51:38: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 10:51:38: Too few paired peaks (28) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 10:51:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Wed, 22 Apr 2020 10:51:38: 6000000 rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:51:42: 7000000 INFO @ Wed, 22 Apr 2020 10:51:47: 8000000 INFO @ Wed, 22 Apr 2020 10:51:51: 9000000 INFO @ Wed, 22 Apr 2020 10:51:56: 10000000 INFO @ Wed, 22 Apr 2020 10:52:00: 11000000 INFO @ Wed, 22 Apr 2020 10:52:04: 12000000 INFO @ Wed, 22 Apr 2020 10:52:07: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 10:52:07: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 10:52:07: #1 total tags in treatment: 5958790 INFO @ Wed, 22 Apr 2020 10:52:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:52:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:52:07: #1 tags after filtering in treatment: 4521225 INFO @ Wed, 22 Apr 2020 10:52:07: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 10:52:07: #1 finished! INFO @ Wed, 22 Apr 2020 10:52:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:52:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:52:07: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 10:52:07: Too few paired peaks (28) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 10:52:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7741031/SRX7741031.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。